Author

Naseem Siraj

Purdue University West Lafayette

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 2 Bioengineering· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Approach:deep learning· 2 Assay:DNA methylation· 2 Approach:statistical model· 2 Assay:long-read sequencing· 1 Approach:mechanistic / dynamical model· 1 Research Focus:protein folding & dynamics· 1 Assay:proteomics· 1

Frequent Co-Authors

Chengde MaoiD· 3 shared Emile J. Batchelder-SchwabiD· 3 shared Anh-Thu Nguyen· 2 shared Hsin‐Chih YehiD· 2 shared Pengyu Y. ReniD· 2 shared S H Kim· 2 shared Siem Yonas· 2 shared Y.-I. CheniD· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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Curved chords = mutual co-authorship

3 shared papersBiophysics

Chengde MaoORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform

Yu-An Kuo, Y.-I. Chen, Naseem Siraj, Yujie He, Zhenglin Yang, Yanxing Wang, Emile J. Batchelder-Schwab, Zeynep Korkmaz, Siem Yonas, Trung D. Nguyen, Soonwoo Hong, Anh-Thu Nguyen, S H Kim, Saeed Seifi, Po‐Hsun Fan, , Hsin‐Chih Yeh

This paper optimizes a DNA-based fluorogenic aptamer (D-FAP) using a screening-and-simulation pipeline on a repurposed sequencing platform, achieving improved fluorescence properties.

ACS Sensors · May 11, 2026Peer-reviewedBiophysics

Lifetime-based multiplexed detection of viral RNA using fluorogenic aptamers

Y R Chen, Yu-An Kuo, Yujie He, Naseem Siraj, Emile J. Batchelder-Schwab, Yin-Jui Chang, Siem Yonas, Yuting Wu, Zhenglin Yang, Anh-Thu Nguyen, S H Kim, Yi Lu, Chengde Mao, Pengyu Y. Ren, Hsin‐Chih Yeh

This paper introduces a fluorescence-lifetime-based multiplexed detection strategy using fluorogenic aptamers to distinguish viral RNA targets with minimal cross-reactivity and spectral overlap.

bioRxiv · Apr 15, 2026 · PreprintBioengineering

Understanding Structural Mechanics of Ligated DNA Crystals via Molecular Dynamics Simulation

Yoo Hyun Kim, Anirudh S. Madhvacharyula, Ruixin Li, Alexander A. Swett, Seongmin Seo, Emile J. Batchelder-Schwab, Naseem Siraj, Chengde Mao, Jong Hyun Choi

The paper uses molecular dynamics simulations to study how ligation patterns affect the mechanical properties of DNA crystals.

Nanoscale Horizons · Jan 1, 2025Peer-reviewedBiophysics